We provide statistical and statistical genetics expertise for large collaborative studies on the genomics and epigenomics of human diseases such as atherosclerosis, diabetes, and obesity. We also perform methodology research in statistical genetics/genomics and genetical systems biology on problems identified with our collaborators.



Principal Investigators

Ina Hoeschele




Ding J, Reynolds LM, Zeller T, et al. Alterations of a Cellular Cholesterol Metabolism Network is a Molecular Feature of Obesity-Related Type 2 Diabetes and Cardiovascular Disease. Diabetes. 2015;In Press.  

Reynolds LM, Ding J, Taylor JR, et al. Transcriptomic profiles of aging in purified human immune cells. BMC genomics. 2015;16:333.  

Yi H, Breheny P, Imam N, Liu Y, Hoeschele I. Penalized multimarker vs. single-marker regression methods for genome-wide association studies of quantitative traits. Genetics. 2015;199:205–222.  


Reyonlds LM, Taylor JR, Ding J, et al. Age-related variations in the methylome associated with gene expression in human monocytes and T cells. Nature Communications. 2014;In Press.  


Liu Y, Ding J, Reynolds LM, et al. Methylomics of gene expression in human monocytes. Human molecular genetics. 2013:ddt356.  


Galindo CL, McIver LJ, Tae H, et al. Sporadic breast cancer patients' germline DNA exhibit an AT-rich microsatellite signature. Genes Chromosomes Cancer. 2011;50:275–283.  http://www.ncbi.nlm.nih.gov/pubmed/21319262

Pinna A, Soranzo N, Hoeschele I, de la Fuente A. Simulating systems genetics data with SysGenSIM. Bioinformatics. 2011;27:2459–2462.  http://www.ncbi.nlm.nih.gov/pubmed/21737438


Huang H, Zhou H, Cheng F, Hoeschele I, Zou F. Gaussian process based bayesian semiparametric quantitative trait Loci interval mapping. Biometrics. 2010;66:222–232.  http://www.ncbi.nlm.nih.gov/pubmed/19459837

Kangas-Kontio T, Kakko S, Tamminen M, et al. Genome scan for loci regulating HDL cholesterol levels in Finnish extended pedigrees with early coronary heart disease. Eur J Hum Genet. 2010;18:604–613.  http://www.ncbi.nlm.nih.gov/pubmed/19935834

Tucker DM, Saghai Maroof MA, Mideros S, et al. Mapping Quantitative Trait Loci for Partial Resistance to Phytophthora sojae in a Soybean Interspecific Cross. Crop Sci.. 2010;50:628–635.  https://dl.sciencesocieties.org/publications/cs/abstracts/50/2/628

Wang H, Waller L, Tripathy S, et al. Analysis of Genes Underlying Soybean Quantitative Trait Loci Conferring Partial Resistance to Phytophthora sojae. Plant Gen.. 2010;3:23–40.  https://www.crops.org/publications/tpg/abstracts/3/1/23

Zou F, Huang H, Lee S, Hoeschele I. Nonparametric Bayesian variable selection with applications to multiple quantitative trait loci mapping with epistasis and gene?environment interaction. Genetics. 2010;186:385–394.  


Armenta JM, Hoeschele I, Lazar IM. Differential Protein Expression Analysis Using Stable Isotope Labeling and PQD Linear Ion Trap MS Technology. Journal of the American Society for Mass Spectrometry. 2009;20:1287–1302.  http://www.sciencedirect.com/science/article/pii/S1044030509001408

Gao G, Allison DB, Hoeschele I. Haplotyping Methods for Pedigrees. Human Heredity. 2009;67:248–266.  http://www.karger.com/DOI/10.1159/000194978

Zhou L, Mideros SX, Bao L, et al. Infection and genotype remodel the entire soybean transcriptome. BMC Genomics. 2009;10:49.  http://www.ncbi.nlm.nih.gov/pubmed/19171053


Bao L, Hoeschele I. [Quality Assessment for Short Oligonucleotide Microarray Data]: Comment. Technometrics. 2008;50:268–271.  http://www.jstor.org/stable/25471485

Gao G, Hoeschele I. A rapid conditional enumeration haplotyping method in pedigrees. Genetics Selection Evolution. 2008;40:25–36.  

Liu B, de la Fuente A, Hoeschele I. Gene network inference via structural equation modeling in genetical genomics experiments. Genetics. 2008;178:1763–1776.  http://www.ncbi.nlm.nih.gov/pubmed/18245846

Tyler BM, Jiang RY, Zhou L, et al. Functional Genomics and Bioinformatics of the Phytophthora sojae Soybean Interaction. In: Gustafson JP, Taylor J, Stacey G, eds. Genomics of Disease. Springer New York; 2008:67–78. Stadler Genetics Symposia Series.  http://dx.doi.org/10.1007%2F978-0-387-76723-9_6


Stock KF, Distl O, Hoeschele I. Bayesian estimation of genetic parameters for multivariate threshold and continuous phenotypes and molecular genetic data in simulated horse populations using Gibbs sampling. BMC Genet. 2007;8:19.  http://www.ncbi.nlm.nih.gov/pubmed/17490471

Stock KF, Distl O, Hoeschele I. Influence of priors in Bayesian estimation of genetic parameters for multivariate threshold models using Gibbs sampling. Genet Sel Evol. 2007;39:123–137.  http://www.ncbi.nlm.nih.gov/pubmed/17306197

Stock KF, Hoeschele I, Distl O. Estimation of genetic parameters and prediction of breeding values for multivariate threshold and continuous data in a simulated horse population using Gibbs sampling and residual maximum likelihood. J Anim Breed Genet. 2007;124:308–319.  http://www.ncbi.nlm.nih.gov/pubmed/17868084


Betthauser JM, Pfister-Genskow M, Xu H, et al. Nucleoplasmin facilitates reprogramming and in vivo development of bovine nuclear transfer embryos. Mol Reprod Dev. 2006;73:977–986.  http://www.ncbi.nlm.nih.gov/pubmed/16604516


Bing N, Hoeschele I. Genetical genomics analysis of a yeast segregant population for transcription network inference. Genetics. 2005;170:533–542.  http://www.ncbi.nlm.nih.gov/pubmed/15781693

Bing N, Hoeschele I, Ye K, Eilertsen KJ. Finite mixture model analysis of microarray expression data on samples of uncertain biological type with application to reproductive efficiency. Vet Immunol Immunopathol. 2005;105:187–196.  http://www.ncbi.nlm.nih.gov/pubmed/15808300

Gao G, Hoeschele I. Approximating identity-by-descent matrices using multiple haplotype configurations on pedigrees. Genetics. 2005;171:365–376.  http://www.ncbi.nlm.nih.gov/pubmed/15965257

Hoeschele I, Li H. A note on joint versus gene-specific mixed model analysis of microarray gene expression data. Biostatistics. 2005;6:183–186.  http://www.ncbi.nlm.nih.gov/pubmed/15772098

Pfister-Genskow M, Myers C, Childs LA, et al. Identification of differentially expressed genes in individual bovine preimplantation embryos produced by nuclear transfer: improper reprogramming of genes required for development. Biol Reprod. 2005;72:546–555.  http://www.ncbi.nlm.nih.gov/pubmed/15483223


de la Fuente A, Bing N, Hoeschele I, Mendes P. Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics. 2004;20:3565–3574.  http://www.ncbi.nlm.nih.gov/pubmed/15284096

Gao G, Hoeschele I, Sorensen P, Du F. Conditional probability methods for haplotyping in pedigrees. Genetics. 2004;167:2055–2065.  http://www.ncbi.nlm.nih.gov/pubmed/15342540


Freyer G, Sorensen P, Kuhn C, Weikard R, Hoeschele I. Search for pleiotropic QTL on chromosome BTA6 affecting yield traits of milk production. J Dairy Sci. 2003;86:999–1008.  http://www.ncbi.nlm.nih.gov/pubmed/12703637

Kakko S, Kelloniemi J, von Rohr P, et al. ATP-binding cassette transporter A1 locus is not a major determinant of HDL-C levels in a population at high risk for coronary heart disease. Atherosclerosis. 2003;166:285–290.  http://www.ncbi.nlm.nih.gov/pubmed/12535741


Du FX, Sorensen P, Thaller G, Hoeschele I. Joint linkage disequilibrium and linkage mapping of quantitative trait loci. Montpellier: Institut National de la Recherche Agronomique (INRA); 2002:1–8.  

Freyer G, KÜHn C, Weikard R, Zhang Q, Mayer M, Hoeschele I. Multiple QTL on chromosome six in dairy cattle affecting yield and content traits. Journal of Animal Breeding and Genetics. 2002;119:69–82.  http://dx.doi.org/10.1046%2Fj.1439-0388.2002.00322.x

Stricker C, Schelling M, Du F, Hoeschele I, Fernández SA, Fernando RL. A comparison of efficient genotype samplers for complex pedigrees and multiple linked loci. Montpellier: Institut National de la Recherche Agronomique (INRA); 2002:1–8.  

von Rohr P, Hoeschele I. Bayesian QTL mapping using skewed Student-t distributions. Genet Sel Evol. 2002;34:1–21.  http://www.ncbi.nlm.nih.gov/pubmed/11929622


Du FX, Hoeschele I. A note on algorithms for genotype and allele elimination in complex pedigrees with incomplete genotype data. Genetics. 2000;156:2051–2062.  http://www.ncbi.nlm.nih.gov/pubmed/11102395

Du FX, Hoeschele I. Estimation of additive, dominance and epistatic variance components using finite locus models implemented with a single-site Gibbs and a descent graph sampler. Genet Res. 2000;76:187–198.  http://www.ncbi.nlm.nih.gov/pubmed/11132412

Thaller G, Hoeschele I. Fine-mapping of quantitative trait loci in half-sib families using current recombinations. Genet Res. 2000;76:87–104.  http://www.ncbi.nlm.nih.gov/pubmed/11006637


Du FX, Hoeschele I, Gage-Lahti KM. Estimation of additive and dominance variance components in finite polygenic models and complex pedigrees. Genetical research. 1999;74:179–187.  


Fuerst-Waltl B, Sölkner J, Essl A, Hoeschele I, Fuerst C. Non-linearity in the genetic relationship between milk yield and type traits in Holstein cattle. Livestock Production Science. 1998;57:41–47.  http://www.sciencedirect.com/science/article/pii/S0301622698001614

Hoeschele I, Grignola FE, Li YI, Thaller G, Uimari P, Zhange Q. MQREML, MQAREML, MPLGIB and NQTLGIB: Software for QTL mapping in outcross or complex pedigrees.; 1998:441–442. Proc. 6th World Cong. Genet. Appl. Livest. Prod., Armidale, Australia 27.  

Zhang Q, Boichard D, Hoeschele I, et al. Mapping quantitative trait loci for milk production and health of dairy cattle in a large outbred pedigree. Genetics. 1998;149:1959–1973.  http://www.ncbi.nlm.nih.gov/pubmed/9691050


Fuerst C, Hoeschele I, Sölkner J, Essl A. The potential use of specific combining ability as selection criterion. Armidale, NSW, Australia; 1997:109–111. 6th World Congr. Genet. Appl. Livest. Prod. 26.  

Fuerst-Waltl B, Soelkner J, Essl A, Hoeschele I. Estimation of non-linear genetic relationships between yield and type traits in Holstein cattle. Armidale, NSW, Australia; 1997:415–418. 6th World Congr. Genet. Appl. Livest. Prod. 23.  

Hoeschele I. Bayesian and residual maximum likelihood statistical gene mapping. Animal Biotechnology. 1997;8:47–54.  http://dx.doi.org/10.1080%2F10495399709525866

Hoeschele I, Uimari P, Grignola FE, Zhang Q, Gage KM. Advances in statistical methods to map quantitative trait loci in outbred populations. Genetics. 1997;147:1445–1457.  

Uimari P, Hoeschele I. Mapping-linked quantitative trait loci using Bayesian analysis and Markov chain Monte Carlo algorithms. Genetics. 1997;146:735–743.  http://www.ncbi.nlm.nih.gov/pubmed/9178021

Zhang FE, Grignola Q. Mapping linked quantitative trait loci via residual maximum likelihood.. 1997.  

Zhang Q, Hoeschele I. Multiple QTL mapping via Residual Maximum Likelihood in outbred populations. Armidale, NSW, Australia; 1997:265–268. 6th World Congr. Genet. Appl. Livest. Prod. 26.  


F.E. G, Hoeschele I, Zhang Q, Thaller G. Mapping Quantitative Trait Loci in outcross populations via Residual Maximum Likelihood. II. A simulation study. Genet. Sel. Evol.. 1996;28:491–504.  

F.E. G, Hoeschele I, Zhang Q, Thaller G. Mapping Quantitative Trait Loci in outcross populations via Residual Maximum Likelihood. I. Methodology. A simulation study. Genet. Sel. Evol.. 1996;28:479–490.  

Hoeschele I, Uimari P, Grignola FE, Zhang Q, Gage KM. Statistical mapping of polygene loci in livestock.; 1996:21–25. Proceedings of the Biometrics Section.  

Thaller G, Dempfle L, Hoeschele I. Investigation of the inheritance of birth defects in swine by complex segregation analysis. Journal of Animal Breeding and Genetics. 1996;113:77–92.  http://dx.doi.org/10.1111%2Fj.1439-0388.1996.tb00593.x

Thaller G, Dempfle L, Hoeschele I. Maximum likelihood analysis of rare binary traits under different modes of inheritance. Genetics. 1996;143:1819–1829.  http://www.ncbi.nlm.nih.gov/pubmed/8844167

Thaller G, Hoeschele I. A Monte Carlo method for Bayesian analysis of linkage between single markers and quantitative trait loci. I. Methodology. Theor Appl Genet. 1996;93:1161–1166.  http://www.ncbi.nlm.nih.gov/pubmed/24162497

Thaller G, Hoeschele I. A Monte Carlo method for Bayesian analysis of linkage between single markers and quantitative trait loci. II. A simulation study. Theor Appl Genet. 1996;93:1167–1174.  http://www.ncbi.nlm.nih.gov/pubmed/24162498

Uimari P, Thaller G, Hoeschele I. A Monte Carlo method for Bayesian analysis of linkage between multiple linked markers and quantitative trait loci. Genetics. 1996;143:1831–1842.  

Uimari P, Zhang Q, Grignola FE, Hoeschele I, Thaller G. Analysis of QTL workshop I granddaughter design data using least-squares, residual maximum likelihood and Bayesian methods. J. Quant. Trait Loci. 1996;2.  


Georges M, Nielsen D, Mackinnon M, et al. Mapping genes controlling milk production: toward marker-assisted selection in livestock. Genetics. 1995;139:907–920.  

Hoeschele I, Tier B. Marginal Maximum Likelihood estimation of variance components of threshold characters via Gibbs sampling. Genet. Sel. Evol.. 1995;27:519–540.  

Hoeschele I, Tier B, Graser HU. Multiple-trait genetic evaluation for one polychotomous trait and several continuous traits with missing data and unequal models. J Anim Sci. 1995;73:1609–1627.  http://www.ncbi.nlm.nih.gov/pubmed/7673055

Weigel DJ, Cassell BG, Hoeschele I, Pearson RE. Multiple-trait prediction of transmitting abilities for herd life and estimation of economic weights using relative net income adjusted for opportunity cost. J Dairy Sci. 1995;78:639–647.  http://www.ncbi.nlm.nih.gov/pubmed/7782520


Georges M, Nielsen D, Mackinnon M, et al. Exploiting progeny-testing to identify polygenes controlling milk production in cattle. Guelph, Canada; 1994. 5th World Congr. Genet. Appl. Livest. Prod. 21.  

Grignola FE, Hoeschele I, Meyer K. Empirical Best Linear Unbiased Prediction to map QTL. Guelph, Canada; 1994:245. 5th World Congr. Genet. Appl. Livest. Prod. 21.  

Hoeschele I. Bayesian QTL mapping via the Gibbs sampler. Guelph, Canada; 1994:241. 5th World Congr. Genet. Appl. Livest. Prod. 21.  

Weigel DJ, Pearson RE, Hoeschele I. Impact of different strategies and amounts of preferential treatment on various methods of bull-dam selection. J Dairy Sci. 1994;77:3163–3173.  http://www.ncbi.nlm.nih.gov/pubmed/7836605


de Boer IJ, Hoeschele I. Genetic evaluation methods for populations with dominance and inbreeding. Theor Appl Genet. 1993;86:245–258.  http://www.ncbi.nlm.nih.gov/pubmed/24193467

Hoeschele I. Elimination of quantitative trait loci equations in an animal model incorporating genetic marker data. Journal of dairy science. 1993;76:1693–1713.  

Hoeschele I, Romano EO. On the use of marker information from granddaughter designs. J Anim Breed Genet. 1993;110:429–449.  http://www.ncbi.nlm.nih.gov/pubmed/21395742

Hoeschele I, Vanraden PM. Bayesian analysis of linkage between genetic markers and quantitative trait loci. II. Combining prior knowledge with experimental evidence. Theor Appl Genet. 1993;85:946–952.  http://www.ncbi.nlm.nih.gov/pubmed/24196144

Hoeschele I, Vanraden PM. Bayesian analysis of linkage between genetic markers and quantitative trait loci. I. Prior knowledge. Theor Appl Genet. 1993;85:953–960.  http://www.ncbi.nlm.nih.gov/pubmed/24196145

Hoeschele I, Vollema AR. Estimation of variance components with dominance and inbreeding in dairy cattle. J Anim Breed Genet. 1993;110:93–104.  http://www.ncbi.nlm.nih.gov/pubmed/21395707

Smothers CD, Pearson RE, Hoeschele I, Funk DA. Herd final score and its relationship to genetic and environmental parameters of conformation traits of United States Holsteins. Journal of dairy science. 1993;76:1671–1677.  


DeStefano AL, Hoeschele I. Utilization of dominance variance through mate allocation strategies. Journal of dairy science. 1992;75:1680–1690.  

VanRaden PM, Lawlor TJ, Short TH, Hoeschele I. Use of reproductive technology to estimate variances and predict effects of gene interactions. J Dairy Sci. 1992;75:2892–2901.  http://www.ncbi.nlm.nih.gov/pubmed/1430491


Hoeschele I. Additive and nonadditive genetic variance in female fertility of Holsteins. J Dairy Sci. 1991;74:1743–1752.  http://www.ncbi.nlm.nih.gov/pubmed/1880275

Hoeschele I, VanRaden PM. Rapid inversion of dominance relationship matrices for noninbred populations by including sire by dam subclass effects. J Dairy Sci. 1991;74:557–569.  http://www.ncbi.nlm.nih.gov/pubmed/2045562

VanRaden PM, Hoeschele I. Rapid inversion of additive by additive relationship matrices by including sire-dam combination effects. J Dairy Sci. 1991;74:570–579.  http://www.ncbi.nlm.nih.gov/pubmed/2045563


Hoeschele I. Potential gain from insertion of major genes into dairy cattle. Journal of dairy science. 1990;73:2601–2618.  

Hoeschele I, Meinert TR. Association of genetic defects with yield and type traits: the weaver locus effect on yield. J Dairy Sci. 1990;73:2503–2515.  http://www.ncbi.nlm.nih.gov/pubmed/2258494


Hoeschele I. A note on local maxima in maximum likelihood, restricted maximum likelihood, and baysian estimation of variance components. Journal of Statistical Computation and Simulation. 1989;33:149–160.  http://dx.doi.org/10.1080%2F00949658908811193

Hoeschele I, Gianola D. Bayesian versus maximum quasi-likelihood methods for sire evaluation with categorical data. Journal of Dairy Science. 1989;72:1569–1577.  

Komender P, Hoeschele I. Use of mixed-model methodology to improve estimation of crossbreeding parameters. Livestock Production Science. 1989;21:101–113.  

Misztal I, Gianola D, Hoeschele I. Note on threshold models with heterogeneous residual variance due to missing information. Genet. Sel. Evol.. 1989;20:511.  


Hoeschele I. Comparison of ?Maximum A-Posteriori Estimation? and ?Quasi Best Linear Unbiased Prediction? with threshold characters. Journal of Animal Breeding and Genetics. 1988;105:337–361.  

Hoeschele I. Genetic evaluation with data presenting evidence of mixed major gene and polygenic inheritance. Theor Appl Genet. 1988;76:81–92.  http://www.ncbi.nlm.nih.gov/pubmed/24231987

Hoeschele I. Statistical techniques for detection of major genes in animal breeding data. Theor Appl Genet. 1988;76:311–319.  http://www.ncbi.nlm.nih.gov/pubmed/24232121

Hoschele I, Rothschild MF, Gianola D. Recursive Estimation of Breeding Values with Categorical Data. Journal of Dairy Science. 1988;71:452–466.  


Foulley JL, Im S, Gianola D, Höschele I. Empirical Bayes estimation of parameters for n polygenic binary traits. Génétique sélection évolution. 1987;19:197–224.  

Höschele I, Gianola D, Foulley JL. Estimation of variance components with quasi-continuous data using Bayesian methods. Journal of Animal Breeding and Genetics. 1987;104:334–349.  


Höschele I, Foulley JL, Colleau JJ, Gianola D. Genetic evaluation for multiple binary responses. Genet. Sel. Evol. 1986;18:299–320.  


Karras K, Hoeschele I, Averdunk G. A first evaluation of stayability in the German Fleckvieh. Der Tierzuchter. 1985;37:116–118.  


Hoeschele I, Niebel E. Population analysis of beef performance characteristics by visual appraisal in young Fleckvieh heifers. Zuechtungskunde (Germany, FR). 1983.